Novel Genes/Genetic Defects in IRDs Our WES analyses have led to identification of two novel IRD genes providing insights into retinal pathways and function. (1) We identified 7 different variants in IDH3A in 4 unrelated families as a cause of Retinitis Pigmentosa (PMID 28412069) (2) We also reported mutation in REEP6, a rod-specific gene in patient with RP and showed in mouse model that REEP6 mediates trafficking of a subset of Clathrin-coated vesicle critical for rod photoreceptor function and survival (PMID 28369466). Additionally, we collaborated with Sam Jocobson to characterize structure, function and disease progression in patients with autosomal recessive RP caused by EYS mutation (PMID 28704921) Genetics of AMD Age-related macular degeneration (AMD) is a leading cause of blindness in the developed world. While many AMD susceptibility variants have been identified, their influence on AMD progression has not been elucidated. We were involved in several different projects, as follows. Using data from two large clinical trials, Age-Related Eye Disease Study (AREDS) and AREDS2, we evaluated the effects of 34 known risk variants on disease progression. We show that for prediction of AMD progression, addition of GRS to the demographic/environmental risk factors considerably improved the prediction performance. Our model for predicting the disease progression risk demonstrated satisfactory performance in both cohorts, and we recommend its use with baseline AMD severity scores plus baseline age, education level, and smoking status, either with or without GRS (PMID 28341650). We are now extending this analysis to genome-wide bivariate time-to-event test for AMD progression with 9 million variants on 2,721 AREDS participants (Yan et al., submitted) We also participated in studying the genetic pleiotrophy between AMD with other complex diseases. We demonstrate a substantial overlap of the genetics of several complex diseases/traits with AMD and provide statistically significant evidence for an additional 20 loci associated with AMD. This highlights the possibility that so far unrelated pathologies may have disease pathways in common (PMID 28347358). To discover additional rare variants and characterize the GWAS locus further, we performed whole genome sequencing of 2,394 cases and 2,393 controls and the analysis is in progress. We have looked into the contribution of rare variants in GWAS loci of sub-types of AMD (Pietraszkiewicz et al., submitted). We have also participated in a deep phenotype association study in AREDS2 reveals specific phenotype association with genetic variants involved in AMD. This shows the association of the SNP at the ARMS2/HTRA1 locus with subretinal/sub-RPE hemorrhage and poorer visual acuity and of SNPs at CFH locus with drusen area may provide new insights in pathophysiological pathways underlying different stages of AMD (Freekje et al., submitted) We also generated WES data in 19 large multigenerational AMD families to ascertain high-penetrance causative allele(s). To enhance the power of analysis, we are collaborating with other groups to extract useful information. Functional Genomic Analysis of AMD Current variants/loci can explain 50-60% of AMD heritability, with ARMS2 and CFH accounting for bulk of the effect. Our collaborative studies suggest increased retinal mitochondrial DNA damage in patients with CFH risk alleles (Ferrington et al. 2016). However, causal variants and underlying mechanisms remain largely unknown for majority of the loci. Thus, we are now focusing on dissection of relative contributions of variants, genes and pathways to AMD pathology. A Reference Transcriptome of Adult Human Retina We have generated a comprehensive reference transcriptome of the normal human retina by RNA-seq analysis of 105 healthy donor samples (from Dr. D Ferrington) We have characterized both annotated coding regions as well as un-annotated transcripts using de novo assembly. This dataset would be valuable for the vision community while designing interventions for retinal diseases. Gene and Pathways Associated with AMD Progression To elucidate genetic underpinnings of progression of AMD phenotypes, AREDS1 data is being examined in collaborative studies. However, lack of longitudinal clinical information in most datasets makes it harder to replicate our findings. Thus, we are taking advantage of transcriptomic studies of 390 donor AMD retinas (197 early, 127 intermediate, 66 advanced). Differential expression, pathway and co-expression analysis has revealed the core transcriptome signature and pathways dysregulated in AMD, providing several novel candidates and insights into the AMD pathobiology. A comprehensive resource of eQTL in retina interpretation of the GWAS findings, and application in risk evaluation and therapeutic interventions remains one of the major challenges for researchers. A large proportion GWAS signals reside in the non-coding region and thus underlying genes/variants are not conspicuous and are most likely to mediate their effect through regulation. To understand this regulation, we used the DNA from 523 donor subjects and genotyped 603,583 markers using UM HUNT Biobank v1.0 chip then obtained the inferred genotypes for 6,554,241 variants using 1000G reference panel through imputation. After adjusting for LD structure, this resulted in 41,364 cis and 8,165 trans eQTL, several of which are in AMD GWAS loci and can help elucidate the causal variants.